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Comparative phylogenetic trees of the Malvaceae based on protein-coding genes from the nuclear genome (16,370 multi-copy by ASTRAL and 1904 single-copy genes by IQ-TREE yielding the same topology and all 100% support values), the chloroplast genome (79 genes) and the mitochondrial genome (37 genes). The trees were rooted by two outgroups ( Vitis vinifera and Carica papaya ). The branch lengths represent the nucleotide substitutions per site, and the values in the nodes represent the bootstrap percentages from IQ-TREE. The confidently well-resolved nodes are indicated by pie charts with the frequencies of three gene tree topologies (q1, q2 and q3; q1 >> q2/q3) calculated in ASTRAL (see Supplementary Fig. 10 for more details). The numbers in brackets indicate the number of genera and species in the given subfamily.

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